Locus 7910

Sequence ID	3L_DroMel_CAF1
Location	21,051,617 – 21,051,797
Length	180
Max. P	0.935649

overview

Window 8

Location	21,051,617 – 21,051,723
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.78
Mean single sequence MFE	-23.40
Consensus MFE	-19.50
Energy contribution	-19.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.39
Structure conservation index	0.83
SVM decision value	0.30
SVM RNA-class probability	0.676650
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051617 106 - 23771897
AAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGAUUCCGAAUCCAA-AACAACGAUAGA-------------CGAAAGACGAGACGCGUCUGUCAAUGACAC
......(((........))).((((.........((((.........)))).............-......((((((-------------((...(......).))))))))..)))).. ( -23.10)
>DroSec_CAF1 106768 105 - 1
AAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAA-AGCCGAUUCCGAAUCCAA-AGCUACGAUAGA-------------CGAAAGACGAGACGCGUCUGUCAAUGACAC
......(((........))).((((....(((..((((.......-.)))).....(....)..-.)))..((((((-------------((...(......).))))))))..)))).. ( -24.20)
>DroSim_CAF1 12980 106 - 1
AAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGAUUCCGAAUCCAA-AGCUACGAUAGA-------------CGAAAGACGAGACGCGUCUGUCAAUGACAC
......(((........))).((((....(((..((((.........)))).....(....)..-.)))..((((((-------------((...(......).))))))))..)))).. ( -23.40)
>DroEre_CAF1 29165 107 - 1
AAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGACUCCGAAACCAAAAACUGCGACAGA-------------CGAAAGACGAGACGCGUCUGUCAAUGACAC
......(((........))).((((.........((((.........))))....................((((((-------------((...(......).))))))))..)))).. ( -25.00)
>DroYak_CAF1 227 120 - 1
AAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGAUUCCGAAACCAAAAACUGCGAUAGACCAAGACGAAAUACGAAAGACGAGACGCGUCUGUCAAUGACAC
................((((((((..........((((.........))))................(((...))).....))).......((.(((((.....))))).))..))))). ( -21.30)
>consensus
AAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGAUUCCGAAUCCAA_AACUACGAUAGA_____________CGAAAGACGAGACGCGUCUGUCAAUGACAC
......(((........))).((((.........((((.........))))........................................((.(((((.....))))).))..)))).. (-19.50 = -19.50 +   0.00)

alignment

secondary structure

dotplot

Window 9

Location	21,051,647 – 21,051,757
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.95
Mean single sequence MFE	-27.94
Consensus MFE	-25.68
Energy contribution	-25.76
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.27
Structure conservation index	0.92
SVM decision value	0.58
SVM RNA-class probability	0.787776
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051647 110 - 23771897
------UGUCUCUUCGGCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGAUUCCGAAUCCAA-AACAACGAUAGA---
------((((.....((((((((((((.(((((....))))...(((...)))....).))))))))..)))).((((.........)))).............-......))))..--- ( -27.70)
>DroSec_CAF1 106798 109 - 1
------UGUCUCUUCGUCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAA-AGCCGAUUCCGAAUCCAA-AGCUACGAUAGA---
------..(((..((((.(((((((((.(((((....))))...(((...)))....).))))))))).(((..((((.......-.)))).....(....)..-.))))))).)))--- ( -24.40)
>DroSim_CAF1 13010 110 - 1
------UGUCUCUUCGGCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGAUUCCGAAUCCAA-AGCUACGAUAGA---
------((((.....((((((((((((.(((((....))))...(((...)))....).))))))))..)))).((((.........)))).............-......))))..--- ( -27.70)
>DroEre_CAF1 29195 117 - 1
UGUGUUUGUUUCUUUGGCCUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGACUCCGAAACCAAAAACUGCGACAGA---
.(((((((((((..((((.((((((((.(((((....))))...(((...)))....).))))))))...))))((((.........)))).....)))))...)))).))......--- ( -29.70)
>DroYak_CAF1 267 114 - 1
------UGUCUCUUCGGCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGAUUCCGAAACCAAAAACUGCGAUAGACCA
------.((((..((((((((((((((.(((((....))))...(((...)))....).))))))))..)))).((((.........))))....................)).)))).. ( -30.20)
>consensus
______UGUCUCUUCGGCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGAAACAAAAGCCGAUUCCGAAUCCAA_AACUACGAUAGA___
......((((.....((((((((((((.(((((....))))...(((...)))....).))))))))..)))).((((.........))))....................))))..... (-25.68 = -25.76 +   0.08)

alignment

secondary structure

dotplot

Window 0

Location	21,051,683 – 21,051,797
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.53
Mean single sequence MFE	-31.06
Consensus MFE	-29.35
Energy contribution	-29.63
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-1.38
Structure conservation index	0.94
SVM decision value	1.20
SVM RNA-class probability	0.929742
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051683 114 + 23771897
UCGCCGUGGCUGUUUUGACUGACAAAUGAAAAUCUCUAUUGGCUAUCGCCAGACAAUCAAAAGCCGAAGAGACA------AACAGCCAUGAGAAGUCGUCUGUCGACGGUUGCAAACUUU
..(((((((((((((((.....))........(((((.((((((.................))))))))))).)------))))))))))...(..((((....))))..)))....... ( -32.93)
>DroSec_CAF1 106833 114 + 1
UCGCCGUGGCUGUUUUGACUGACAAAUGAAAAUCUCUAUUGGCUAUCGCCAGACAAUCAAAAGACGAAGAGACA------CACAGCCAUGAGAAGUCGUCUGUCGCCGGUUGCAAACCUU
..(((((((((((((((.....))))......(((((.(((((....)))))....((....))...)))))..------.)))))))))(((.....)))...)).(((.....))).. ( -26.50)
>DroSim_CAF1 13046 114 + 1
UCGCCGUGGCUGUUUUGACUGACAAAUGAAAAUCUCUAUUGGCUAUCGCCAGACAAUCAAAAGCCGAAGAGACA------AACAGCCAUGAGAAGUCGUCUGUCGACGGUUGCAAACUUU
..(((((((((((((((.....))........(((((.((((((.................))))))))))).)------))))))))))...(..((((....))))..)))....... ( -32.93)
>DroEre_CAF1 29232 120 + 1
UCGCCGUGGCUGUUUUGACUGACAAAUGAAAAUCUCUAUUGGCUAUCGCCAGACAAUCAAAGGCCAAAGAAACAAACACAAACAGCCAUGAGAAGUCGUCUGUCGACGGUUGCAAACUUU
..(((((((((((((((..((....((....)).(((.((((((.................)))))))))..))..)).)))))))))))...(..((((....))))..)))....... ( -30.03)
>DroYak_CAF1 307 114 + 1
UCGCCGUGGCUGUUUUGACUGACAAAUGAAAAUCUCUAUUGGCUAUCGCCAGACAAUCAAAAGCCGAAGAGACA------AACAGCCAUGAGAAGUCGUCUGUCGACGGUUGCAAACUUU
..(((((((((((((((.....))........(((((.((((((.................))))))))))).)------))))))))))...(..((((....))))..)))....... ( -32.93)
>consensus
UCGCCGUGGCUGUUUUGACUGACAAAUGAAAAUCUCUAUUGGCUAUCGCCAGACAAUCAAAAGCCGAAGAGACA______AACAGCCAUGAGAAGUCGUCUGUCGACGGUUGCAAACUUU
..(((((((((((((((.....))))......(((((.((((((.................))))))))))).........)))))))))...(..((((....))))..)))....... (-29.35 = -29.63 +   0.28)

alignment

secondary structure

dotplot

Window 1

Location	21,051,683 – 21,051,797
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.53
Mean single sequence MFE	-34.02
Consensus MFE	-30.14
Energy contribution	-30.38
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.58
Structure conservation index	0.89
SVM decision value	1.25
SVM RNA-class probability	0.935649
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21051683 114 - 23771897
AAAGUUUGCAACCGUCGACAGACGACUUCUCAUGGCUGUU------UGUCUCUUCGGCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGA
............((((((((((((.((......)).))))------)))).....((((((((((((.(((((....))))...(((...)))....).))))))))..))))..)))). ( -34.50)
>DroSec_CAF1 106833 114 - 1
AAGGUUUGCAACCGGCGACAGACGACUUCUCAUGGCUGUG------UGUCUCUUCGUCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGA
..(((.....)))(((((((((.((..((((.(((((((.------((((.....(((....))).....)))))))))))...))))...)).)))))).)))......((....)).. ( -33.60)
>DroSim_CAF1 13046 114 - 1
AAAGUUUGCAACCGUCGACAGACGACUUCUCAUGGCUGUU------UGUCUCUUCGGCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGA
............((((((((((((.((......)).))))------)))).....((((((((((((.(((((....))))...(((...)))....).))))))))..))))..)))). ( -34.50)
>DroEre_CAF1 29232 120 - 1
AAAGUUUGCAACCGUCGACAGACGACUUCUCAUGGCUGUUUGUGUUUGUUUCUUUGGCCUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGA
.....((((...((((....))))........((((((((((((...(((((((((((..(((.........)))..))))).))))))...))).((.....)))))))))))..)))) ( -33.00)
>DroYak_CAF1 307 114 - 1
AAAGUUUGCAACCGUCGACAGACGACUUCUCAUGGCUGUU------UGUCUCUUCGGCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGA
............((((((((((((.((......)).))))------)))).....((((((((((((.(((((....))))...(((...)))....).))))))))..))))..)))). ( -34.50)
>consensus
AAAGUUUGCAACCGUCGACAGACGACUUCUCAUGGCUGUU______UGUCUCUUCGGCUUUUGAUUGUCUGGCGAUAGCCAAUAGAGAUUUUCAUUUGUCAGUCAAAACAGCCACGGCGA
.....((((...((((....))))........(((((((........(((.....))).((((((((.(((((....))))...(((...)))....).)))))))))))))))..)))) (-30.14 = -30.38 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:28 2006